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Chuanyu Sun and Paul VanRaden National Association of Animal Breeders (NAAB) Animal Genomics and Improvement Laboratory (AGIL) Genomic Relationships for Mating Programs Chuanyu Sun 08/05/2014 CDCB Open Session for Industry

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Introduction Computerized mating programs have helped breeders reduce pedigree inbreeding by identifying matings between animals with fewer ancestors in common than average In genomic era, dense single nucleotide polymorphism (SNP) markers across the whole genome have been widely used for genomic selection Pedigree relationship Genomic relationship

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Introduction Pedigree relationship Genomic relationship 40925026 00000021111120022002111011111201110101111001 52110921 2000200101001120220021100201200012212001120 54304711 2100002021102002200200002202020220022200200 The realized relationship The expected relationship

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Introduction Inbreeding should be controlled on the same basis as used to estimate breeding values (Sonesson et al. 2012) Pedigree-based inbreeding control with traditional pedigree- based method estimated breeding values Genome-based inbreeding control with genome-based estimated breeding values New programs to minimize genomic inbreeding by comparing genotypes of potential mates should be developed and implemented by breed associations, AI organizations, and on-farm software providers

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Genomic relationship The Genomic relationship file given bulls and cows ID is ready to create routinely by CDCB since Aug, 2014 This file includes all the genotyped females and a list of bulls

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Genomic relationship Which bulls were included ? HO: The 3,300 potential sires are: 800 A - Active bulls 500 I Inactive bulls that breeders are still using 1000 G - Genomic young sire semen being marketed. 1000 C - High Ranking Elite sires Collected but not yet made available 1.Within each category, bulls would be sorted by NM$ with the highest ones taken first 2.Extra criteria: the top 500 Inactive bulls would also need to have a minimum production and type reliability of at least 95%. This way is to ensure that we are selecting the popular Inactive bulls. 3.Other breeds limit reliability >90%

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Genomic relationship Each approved CDCB member organization would receive their own copy of the file One breed one file The CDCB would create the large file 3 times per year. Then at each monthly genomic update, providing a monthly update file for new females with the Previously identified bulls

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How to earn benefit Mating strategies

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How to earn benefit Mean expect progeny values (EPV) GLNM is Genomic lifetime net merit B LNM is defined as the loss of LNM per 1% inbreeding, B LNM =$23.11 EFI is expected future inbreeding, G sire,dam is the genomic relationship between sire and dam

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How to earn benefit Mating strategies Random mating (RD) EPV ij females bulls Linear programming (LP) Sequential selection of least-related mates (SM)

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How to earn benefit Mating programsBrown SwissJerseyHolstein Males850 females79500 Example data

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How to earn benefit Example data increased Progeny values Selected bullsMating method Mate Inbreeding source EPV 2 ($) Brown SwissHolsteinJersey Top 50 for genomic LNMLinear programmingGenomic 205494358 Pedigree 184462326 Sequential least-related 3 Genomic 181474333 Pedigree 175450312 Random 138422255 Top 50 for traditional LNMLinear programmingGenomic 158393307 Pedigree 136363274 Sequential least-related 2 Genomic 127372278 Pedigree 124350263 Random 107314214 Random 50Linear programmingGenomic 647078 Pedigree 434042 Genomic 647078 Pedigree 454041 Sequential least-related 2 Genomic 373646 Pedigree 272129 Genomic 323946 Pedigree 222427 Random000 2 Relative to randomly selected bulls that were randomly mated 3 Pryce et al. (2012)

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How to earn benefit Example data reducing progeny inbreeding Selected bullsMating method Mate Inbreeding source Progeny inbreeding (%) Brown SwissHolsteinJersey Top 50 for genomic LNMLinear programmingGenomic 6.945.173.72 Pedigree 7.876.585.12 Sequential least-relatedGenomic 7.976.034.78 Pedigree 8.277.095.70 Random 9.838.318.17 Top 50 for traditional LNMLinear programmingGenomic 6.114.873.41 Pedigree 7.076.154.82 Sequential least-relatedGenomic 7.455.794.66 Pedigree 7.606.725.32 Random 8.368.307.43 Random 50Linear programmingGenomic 6.644.463.65 Pedigree 7.565.775.22 Genomic 6.644.463.65 Pedigree 7.495.785.26 Sequential least-relatedGenomic 7.835.975.04 Pedigree 8.266.585.76 Genomic 8.055.845.05 Pedigree 8.476.485.86 Random9.307.517.04

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1. Expected progeny value was higher when genomic rather than pedigree relationship was used as the mate inbreeding source. 2. Expected progeny value was higher for linear programming than the sequential method, and both of those methods were better than random mating. 3. Expected progeny value was higher when top 50 mated bulls were selected based on genomic LNM rather than traditional LNM or random. 4. Mean genomic inbreeding of progeny was lowest when genomic relationship was used other than pedigree relationship 5. LP is better than SM and RD on control inbreeding of progeny How to earn benefit Example data summaries

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How to earn benefit Total annual value (based on Oct, 2012 data): ($494 - $462)(120989) = $3,871,648 Only by replacing Pedigree relationship using Genomic relationship Selected bullsMating method Mate Inbreeding source EPV ($) Brown SwissHolsteinJersey Top 50 for genomic LNMLinear programming Genomic 205 494 358 Pedigree 184 462 326 Sequential least-related 3 Genomic 181474333 Pedigree 175450312 Random138422255

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How to earn benefit Economic benefits will continue to grow as more females are genotyped ($494 - $462)(249877 ) = $7,996,064

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Software Implement Genomic relationship Linear programming GLPK http://www.gnu.org/software/glpk/ Rglpk http://cran.r-project.org/web/packages/Rglpk/index.html lpSolve http://cran.r-project.org/web/packages/lpSolve/index.html Rsymphony http://cran.r-project.org/web/packages/Rsymphony/index.html

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Software Implement Available The matingProgram package includes two executable files: matingProgram_S1 matingProgram_S2 This package performs 3 functions: I.Create relationship files given bulls ID and female ID II.Create relationship and mating plans files given bulls ID and female ID III.Make mating plans given bulls ID, female ID and relationship file The matingProgram package includes two executable files: matingProgram_S1 matingProgram_S2 This package performs 3 functions: I.Create relationship files given bulls ID and female ID II.Create relationship and mating plans files given bulls ID and female ID III.Make mating plans given bulls ID, female ID and relationship file

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Inputs Outputs HOUSA000069981349 HOUSA000069560690 HOUSA000070625846 HOUSA000064633877 HOUSA000053668601 HOUSA000134954851 HOUSA000061834459 HOUSA000061839286 HOUSA000061845599 HOUSA000061845646 HOUSA000061845655 HOUSA000061845681 HOUSA000061845689 HOUSA000061845706 HOUSA000061845722 HOUSA00035SHE7944 HOUSA00035SHE7943 HOUSA00035SHE7948 HOUSA00035SHE7949 Software Implement

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Discussions Type trait I. Nonlinear merit function II. M=c + a G + bG 2 (b